Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.01 kDa 
• Atom Count: 1055 
• Modelled Residue Count: 160 
• Deposited Residue Count: 160 
• Unique protein chains: 1

2K3N

Solution structure of the type 1 repetitive domain (TUSP1-RP1) of the egg case silk from Nephila Antipodiana

• PDB DOI: 10.2210/pdb2K3N/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Trichonephila antipodiana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-14 Released: 2009-06-02 
• Deposition Author(s): Lin, Z., Huang, W., Fan, J., Yang, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of eggcase silk protein and its implications for silk fiber formation

Lin, Z., Huang, W., Zhang, J., Fan, J.S., Yang, D.

(2009) Proc Natl Acad Sci U S A 106: 8906-8911

• PubMed: 19458259 
• DOI: 10.1073/pnas.0813255106
• Primary Citation of Related Structures:  
  2K3N, 2K3O, 2K3P, 2K3Q


• PubMed Abstract: 
  

Spider silks are renowned for their excellent mechanical properties and biomimetic and industrial potentials. They are formed from the natural refolding of water-soluble fibroins with alpha-helical and random coil structures in silk glands into insoluble fibers with mainly beta-structures. The structures of the fibroins at atomic resolution and silk formation mechanism remain largely unknown. Here, we report the 3D structures of individual domains of a approximately 366-kDa eggcase silk protein that consists of 20 identical type 1 repetitive domains, one type 2 repetitive domain, and conserved nonrepetitive N- and C-terminal domains. The structures of the individual domains in solution were determined by using NMR techniques. The domain interactions were investigated by NMR and dynamic light-scattering techniques. The formation of micelles and macroscopic fibers from the domains was examined by electron microscopy. We find that either of the terminal domains covalently linked with at least one repetitive domain spontaneously forms micelle-like structures and can be further transformed into fibers at > or = 37 degrees C and a protein concentration of > 0.1 wt%. Our biophysical and biochemical experiments indicate that the less hydrophilic terminal domains initiate the assembly of the proteins and form the outer layer of the micelles whereas the more hydrophilic repetitive domains are embedded inside to ensure the formation of the micelle-like structures that are the essential intermediates in silk formation. Our results establish the roles of individual silk protein domains in fiber formation and provide the basis for designing miniature fibroins for producing artificial silks.

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Related Citations: 

• Resonance Assignments of a Repeated Domain of the Egg Case Silk from Nephila Antipodiana
  Lin, Z., Huang, W., Yang, D.
  () To be published --: --

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Organizational Affiliation: 

Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TuSp1	A	160	Trichonephila antipodiana	Mutation(s): 0  Gene Names: EGGCASE SILK GENE
UniProt
Find proteins for Q1I128 (Trichonephila antipodiana) Explore Q1I128  Go to UniProtKB:  Q1I128

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2K3N Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-14 
• Released Date: 2009-06-02 
Deposition Author(s): Lin, Z., Huang, W., Fan, J., Yang, D.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations, Experimental preparation